Re: [R] How to read and write an S4 class
see ?dput ?save e.g. setClass(track, representation(x=numeric, y=numeric)) x - new(track, x=1:4, y=5:8) # save as binary fn - tempfile() save(x, ascii=FALSE, file=fn) rm(x) load(fn) x # save as ASCII save(x, ascii=TRUE, file=fn) # ASCII text representation from which to regenerate the data dput(x, file=fn) y - dget(fn) R_help Help wrote: Hi, I have an object in S4 class. Is there anyway that I can write to a file and read it back to R? Thank you. adschai __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-0fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to stop function printing unwanted output?
?capture.output
so with the given example this line should do what you wanted while avoiding
the output file
dummy - capture.output(comparison - LSD.test(yield,virus,df,MSerror,
p.adj=bonferroni,
group=FALSE, main=Yield of sweetpotato\ndealt with different virus))
Matthias
David Winsemius wrote:
On Aug 6, 2009, at 12:24 PM, Erik Iverson wrote:
In my example, I don't want LSD.test to print any output, I just want
to use some of it later... How to stop it printing anything?
?invisible
I'm not sure that works in this situation:
test - function() {
print(output)
}
test()
invisible(test())
Both of the above still print out output, which I think is the
original problem. The invisible function will not print the value of a
function, but if there is an explicit print call within the
function, that will of course happen, since the value hasn't been
returned at that point. However, we don't know the original problem
since LSD.test is not defined, and therefore the example is not
reproducible. I assume within the function, it is printing out some
values using print or cat? We just have to guess though.
Maybe the answer is in ?sink ??
Quite right. A search suggests that LSD.test is from package agricolae
and it does have several points at which cat() and print() would be
subverting my intent. So the answer would be to sink it somewhere that
the sun does not shine and then unsink or would that be resurface?
With the example on the LSD.test help page:
sink(file=undesired.txt)
comparison - invisible( LSD.test(yield,virus,df,MSerror,
p.adj=bonferroni, group=FALSE,
+ main=Yield of sweetpotato\ndealt with different virus) )
sink()
comparison
trtmeans M N std.err
1 cc 24.4 3 2.084067
2 fc 12.86667 3 1.246774
3 ff 36.3 3 4.233727
4 oo 36.9 3 2.482606
Erik
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-0fax:+49-30-24345-555
http://www.epigenomics.com matthias.bur...@epigenomics.com
--
Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861
Vorstand: Geert Nygaard (CEO/Vorsitzender)
Oliver Schacht PhD (CFO)
Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bug in package.skeleton, R 2.9.0?
Daniel Klevebring wrote: Bump Anyone? Thanks Daniel On 13 jul 2009, at 10.57, Daniel Klevebring wrote: Dear all, I am using package.skeleton to build a small packages of misc function for personal use. I have recently discovered that the option force=TRUE doesn't seem to do what is meant to do. Here's what I'm doing: setwd(/Users/danielk/Documents/R/packages/dk) files - paste(codebase, dir(codebase, pattern=.R), sep=/) package.skeleton(name=dk, force=TRUE, code_files=files) Creating directories ... Creating DESCRIPTION ... Creating Read-and-delete-me ... Copying code files ... Making help files ... Done. Further steps are described in './dk/Read-and-delete-me'. Now, everything seems fine, but changes to files in me codebase folder, doesn't come along if the folder dk/R already contains the files, even though I use force=TRUE. If I remove the dk/R folder or the dk folder altogether, the changes come along so to me it seems that it's the overwrite part that doesn't work as it should - or am I doing something wrong here? To me, it seems that the function safe.dir.create (which is defined in package.skeleton never overwrites folders, yielding force=TRUE useless. from the help on package.skeleton force: If 'FALSE' will not overwrite an existing directory. which could be clearer in that package.skeleton will stop with an error if the top level directory, i.e. 'dk' in your case, exists and you had specified force=FALSE. But it will not overwrite the existing directory 'dk' with force=TRUE as you observed. Looking at the code it is clear that file.copy is used to copy the code files and that has per default overwrite=FALSE so your existing code files will not be overwritten. With the current implementation package.skeleton will not do what you intended. There are many ways to workaround e.g. fn - dir(codebase, pattern=.R, full.names=TRUE) file.remove( list.files(path=file.path(dk, R), pattern=\\.R, full.names=TRUE)) package.skeleton(name=dk, force=TRUE, code_files=fn) Matthias See below for sessionInfo. Thanks a bunch Daniel sessionInfo() R version 2.9.0 (2009-04-17) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.9.0 -- Contact information: Daniel Klevebring M. Sc. Eng., Ph.D. Student Dept of Gene Technology Royal Institute of Technology, KTH SE-106 91 Stockholm, Sweden Visiting address: Roslagstullsbacken 21, B3 Delivery address: Roslagsvägen 30B, 104 06, Stockholm Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075, SE-10450 Stockholm E-mail: dan...@biotech.kth.se Phone: +46 8 5537 8337 (Office) Phone: +46 704 71 65 91 (Mobile) Web: http://www.biotech.kth.se/genetech/index.html Fax: +46 8 5537 8481 -- Contact information: Daniel Klevebring M. Sc. Eng., Ph.D. Student Dept of Gene Technology Royal Institute of Technology, KTH SE-106 91 Stockholm, Sweden Visiting address: Roslagstullsbacken 21, B3 Delivery address: Roslagsvägen 30B, 104 06, Stockholm Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075, SE-10450 Stockholm E-mail: dan...@biotech.kth.se Phone: +46 8 5537 8337 (Office) Phone: +46 704 71 65 91 (Mobile) Web: http://www.biotech.kth.se/genetech/index.html Fax: +46 8 5537 8481 MSN messenger: klevebr...@msn.com [[alternative HTML version deleted]] ATT1.txt -- Contact information: Daniel Klevebring M. Sc. Eng., Ph.D. Student Dept of Gene Technology Royal Institute of Technology, KTH SE-106 91 Stockholm, Sweden Visiting address: Roslagstullsbacken 21, B3 Delivery address: Roslagsvägen 30B, 104 06, Stockholm Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075, SE-10450 Stockholm E-mail: dan...@biotech.kth.se Phone: +46 8 5537 8337 (Office) Phone: +46 704 71 65 91 (Mobile) Web: http://www.biotech.kth.se/genetech/index.html Fax: +46 8 5537 8481 MSN messenger: klevebr...@msn.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-0fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht
Re: [R] if condition doesn't evaluate to True/False
see
?is.null
e.g.
if( is.null(sub_grp_whr_cls_data[sbgrp_no, 1]) )
{
your code
}
Moumita Das wrote:
Hi friends,
Please help me with this bug.
*Bug in my code:*
In this variable sub_grp_whr_cls_data[sbgrp_no,1] I store the where
clause.every sub group has a where condition linked with it.
Database1
Where clause was not found for a particular subgroup,
sub_grp_whr_cls_data[sbgrp_no,1] value was NULL
So the condition (*sub_grp_whr_cls_data[sbgrp_no,1]==NULL ||
sub_grp_whr_cls_data[sbgrp_no,1]==*) should evaluate to TRUE ,but it
evaluated to NA
So the if block where I used the the condition threw error
If(*sub_grp_whr_cls_data[sbgrp_no,1]==NULL ||
sub_grp_whr_cls_data[sbgrp_no,1]==*)
i.e if(NA)
Error:--
Error in if (sub_grp_whr_cls_data[sbgrp_no, 1] == NULL ||
sub_grp_whr_cls_data[sbgrp_no, :
missing value where TRUE/FALSE needed
Comments:-- but when there ‘s no where clause value the condition
(sub_grp_whr_cls_data[sbgrp_no,1]==NULL
||sub_grp_whr_cls_data[sbgrp_no,1]==) should automatically evaluate to *
TRUE*
Database2
Where clause was found for a particular subgroup
The condition (sub_grp_whr_cls_data[sbgrp_no,1]==NULL
||sub_grp_whr_cls_data[sbgrp_no,1]==) evaluated to FALSE
So if (sub_grp_whr_cls_data[sbgrp_no,1]==NULL
||sub_grp_whr_cls_data[sbgrp_no,1]==) is
If (FALSE) ,control goes to the else part.
This is exactly what is expected of the program.
*QUERY:-- **If the condition evaluates to FALSE when a where condition is
available why doesn’t it evaluate to TRUE when a where condition available
is NULL or no where condition is available.*
Here I have taken the example of two databases where I tried to get the
where clause for subgroup 1.In case of Database1 it was not available in
case of Databse2 it was available.But the problem may appear for the same
database also, when where clause is available for say one subgroup and not
for the other.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-0fax:+49-30-24345-555
http://www.epigenomics.com matthias.bur...@epigenomics.com
--
Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861
Vorstand: Geert Nygaard (CEO/Vorsitzender)
Oliver Schacht PhD (CFO)
Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] if condition doesn't evaluate to True/False
Petr PIKAL wrote:
Hi
r-help-boun...@r-project.org napsal dne 29.04.2009 17:05:01:
see
?is.null
e.g.
if( is.null(sub_grp_whr_cls_data[sbgrp_no, 1]) )
{
your code
}
It probably will not work as
sub_grp_whr_cls_data[sbgrp_no,1]==NULL
implicates that there is character value NULL. I am not sure if you can
get NULL as a part of some object. I tried and failed.
See what you get
x- c(1,2,3, NULL)
Regards
Petr
thanks for pointing this out clearly, I had thought only about making the
comparison
return a logical for use in the expression.
On hindsight it seems implausible to ever get NULL in the matrix/data frame.
(DONT USE
playing around I found the following abuse to work
m - as.data.frame(diag(3))
m[[3]][3] - list(NULL)
is.null(m[3,3][[1]])
[1] TRUE
)
Regards,
Matthias
Moumita Das wrote:
Hi friends,
Please help me with this bug.
*Bug in my code:*
In this variable sub_grp_whr_cls_data[sbgrp_no,1] I store the where
clause.every sub group has a where condition linked with it.
Database1
Where clause was not found for a particular subgroup,
sub_grp_whr_cls_data[sbgrp_no,1] value was NULL
So the condition (*sub_grp_whr_cls_data[sbgrp_no,1]==NULL ||
sub_grp_whr_cls_data[sbgrp_no,1]==*) should evaluate to TRUE ,but it
evaluated to NA
So the if block where I used the the condition threw error
If(*sub_grp_whr_cls_data[sbgrp_no,1]==NULL ||
sub_grp_whr_cls_data[sbgrp_no,1]==*)
i.e if(NA)
Error:--
Error in if (sub_grp_whr_cls_data[sbgrp_no, 1] == NULL ||
sub_grp_whr_cls_data[sbgrp_no, :
missing value where TRUE/FALSE needed
Comments:-- but when there ‘s no where clause value the condition
(sub_grp_whr_cls_data[sbgrp_no,1]==NULL
||sub_grp_whr_cls_data[sbgrp_no,1]==) should automatically evaluate
to *
TRUE*
Database2
Where clause was found for a particular subgroup
The condition (sub_grp_whr_cls_data[sbgrp_no,1]==NULL
||sub_grp_whr_cls_data[sbgrp_no,1]==) evaluated to FALSE
So if (sub_grp_whr_cls_data[sbgrp_no,1]==NULL
||sub_grp_whr_cls_data[sbgrp_no,1]==) is
If (FALSE) ,control goes to the else part.
This is exactly what is expected of the program.
*QUERY:-- **If the condition evaluates to FALSE when a where
condition is
available why doesn’t it evaluate to TRUE when a where condition
available
is NULL or no where condition is available.*
Here I have taken the example of two databases where I tried to get
the
where clause for subgroup 1.In case of Database1 it was not available
in
case of Databse2 it was available.But the problem may appear for the
same
database also, when where clause is available for say one subgroup and
not
for the other.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-0fax:+49-30-24345-555
http://www.epigenomics.com matthias.bur...@epigenomics.com
--
Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861
Vorstand: Geert Nygaard (CEO/Vorsitzender)
Oliver Schacht PhD (CFO)
Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-0fax:+49-30-24345-555
http://www.epigenomics.com matthias.bur...@epigenomics.com
--
Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861
Vorstand: Geert Nygaard (CEO/Vorsitzender)
Oliver Schacht PhD (CFO)
Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
Re: [R] Error in var(x, na.rm = na.rm) : no complete element pairs
Carlos Morales wrote: Hello, I still have the same error which I have written in the Subject field, I leave here the code and I hope you can help me with this: [removed] the lengthy code example does not make it easier to help you, in particular without the data you used. All the commented out code should have been removed before posting. My guess is that you use R 2.8.0 and generate a vector s which contains only NAs. Try to inspect your function filter.clones by putting a browser() call somewhere before the sd() call and run it again. See ?browser and ?trace. And you could vectorize this (and other parts), e.g. the last loop would be rewritten as tripliclones.info$Estandar_desviation - apply(tripliclones.info[ ,2:4], 1, function(x) sd(as.numeric(x), na.rm=TRUE)) Regards, Matthias R version 2.7.1 (2008-06-23) b - rep(NA,4) sd(b) Error in var(x, na.rm = na.rm) : missing observations in cov/cor sd(b, TRUE) Error in var(x, na.rm = na.rm) : no complete element pairs R version 2.8.1 (2008-12-22) b- rep(NA,4) sd(b) [1] NA sd(b, TRUE) [1] NA -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-0fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package tests
Hi Nathan, in addition to what others have already mentioned there is some documentation in the Writing R Extensions Manual: - on the supported structure of packages, indicating where test code might be added http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Package-subdirectories - and the recommended standard approach to check a package http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Checking-and-building-packages and a wiki article on how to combine the standard check (viz R CMD check) with any of the unit testing approaches http://wiki.r-project.org/rwiki/doku.php?id=developers:runits=unit%20test Examples for the standard approach employed by R can be found in the R source repository https://svn.r-project.org/R/trunk/src/library/stats/tests/ and for unit test based checking e.g. Rmetrics http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/?root=rmetrics or BioConductor examples https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase/inst/UnitTests/ where you need the access info provided here http://wiki.fhcrc.org/bioc/DeveloperPage Regards, Matthias Nathan S. Watson-Haigh wrote: I was wondering if anyone could point me in the right direction for reading up on writing tests in R. I'm writing some functions for inclusion into a package and would like to test them to ensure they're doing what I expect them to do. Are these approaches used for testing packages in CRAN? Cheers, Nathan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-371 fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
